It is likely a bacterial rot such as Erwinia. Cut out the rot again, place the plants in a shaded dry location and refrain from watering for a couple weeks. After 2 weeks, wipe the leaves with a paper towel and hydrogen peroxide. Wait a day or two, then resume watering just the roots, very carefully, no water on the leaves. Keep the plants under observation each day, looking for signs that the rot has returned.
After a few more weeks you can treat the plant normally, though I would still plant to keep it out of the rain and in the shade for a while.
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